All Classes
AAIdentityFeature
AAIdentityFeatureAbsolute
AAIdentityFeatureRelative
AAIntensityRankScore
AaMass
AAMS2MzFidelityScore
AaOccurrence
AAPropertyFeature
AAPropertyFeatureAbsolute
AAPropertyFeatureRelative
AAPropertyRelationshipFeature
AAPropertyRelationshipFeature.Relationship
AASequenceFeature
AASequenceFeature.Function
AASequenceImpl
AaSubstitutionMatrix
AaSubstitutionMatrixTableModel
AbstractIdentificationParametersCli
AdvancedProteinDatabaseDialog
Advocate
Advocate.AdvocateType
Alanine
AlgorithmSettingsDialog
AlignedListCellRenderer
AlignedTableCellRenderer
AlignmentBlock
AlternateRowColoursJTable
AmbiguousSequenceIterator
AminoAcid
AminoAcid.Property
AminoAcidPattern
AminoAcidPatternDialog
AminoAcidSequence
AminoAcidSubstitution
AndromedaIdfileReader
AndromedaParameters
AndromedaParameters.AndromedaDecoyMode
AndromedaSettingsDialog
AnnotationSettings
AnnotationSettings.IntensityThresholdType
AnnotationSettingsDialog
AplExporter
Arginine
AScore
Asparagine
AsparticAcid
Atom
AtomChain
AtomChainDialog
AtomImpl
AtomPanel
B
BareBonesBrowserLaunch
BasicMathFunctions
BigFunctions
BigMathUtils
BinaryArrayImpl
BinningFilter
BinomialDistribution
BiomartMapping
BoxedObject
BugReport
ByteArrayRenderer
Carbon
Charge
ChromatogramPanel
ColumnTypeConverter
CometParameters
CometParameters.CometOutputFormat
CometSettingsDialog
CommandLineExceptionHandler
CommandLineParser
CommandLineUtils
CommandParameter
CompareVersionNumbers
CompareVersionNumbers
ComplementarityScore
ComplementaryIonAminoAcidFeature
ComplementaryIonFeature
CompomicsTools
CompomicsWrapper
ConfigurationFile
Connectable
ConnectionDialog
ConnectionManager
Constants
Constructors
Contact
ContactGroup
CvTerm
Cysteine
DasAlignment
DasAnnotationServerAlingmentReader
DasAnnotationServerResultReader
DasFeature
DataRoc
DataRoc.RocInterpolation
DateChooser
DatFileFilter
DBAccessor
DBAccessorGenerator
DBElement
DBMetaData
DBResultSet
DefaultOutputLoggerImplementation
DefaultSpectrumAnnotation
DefaultStyle
Deleteable
DeleteableCode
Deletion
DerbyUtil
DigestionPreferences
DigestionPreferences.CleavagePreference
DigestionPreferences.Specificity
DirecTagIdfileReader
DirecTagParameters
DirecTagSettingsDialog
Distribution
DistributionRoc
DoubleMatrix
DownloadingUtil
DownloadLatestZipFromRepo
DtaFileFilter
DualEnzyme
DummyFrame
DummyParameters
Duration
ElementaryElement
ElementaryIon
EnsemblGenomesSpecies
EnsemblGenomesSpecies.EnsemblGenomeDivision
EnsemblSpecies
EnsemblVersion
Enzyme
Enzyme
EnzymeFactory
EnzymesCLI
EnzymesCLIInputBean
EnzymesCLIParams
EnzymeSelectionDialog
ExcelWriter
ExceptionHandler
ExperimentIO
ExperimentObject
Export
ExportFactory
ExportFeature
ExportFormat
ExportFormatSelectionDialog
ExportGraphicsDialog
ExportScheme
ExportWriter
FastaFileFilter
FastaIndex
FeaturesGenerator
FeaturesMap
FeaturesMapManager
FeedBack
FeedBack.FeedBackType
FileAdapter
FileAndFileFilter
FileDAO
FileDisplayDialog
FileFilterUtils
FileLoggerImplementation
FilenameExtensionFilter
FileSelectionDialog
FileSystemAccessor
FileType
Filter
FilterItem
FilterItemComparator
FindPdbForUniprotAccessions
Flamable
FlamableJFrame
Fluorine
FMIndex
FolderMonitor
ForwardIonAminoAcidFeature
ForwardIonFeature
FractionSettings
FractionSettingsDialog
FragmentAnnotator
FragmentAnnotatorNL
FragmentationMethod
FragmentIonTable
FragmentIonTableCellRenderer
FragmentItensityPredictor
FrameExceptionHandler
FTP
FTPClient
FtpConnectionException
FTPDownloader
FtpLoginException
FtpProtocolException
GeneDetailsDialog
GeneFactory
GeneMapping
GeneMaps
GenePreferences
GenePreferencesDialog
GeneratorException
GettersAndSetters
GlutamicAcid
Glutamine
Glycan
Glycine
GoDomains
GoMapping
GraphicsPanel
GraphicsPanel.DrawingStyle
GraphicsPanel.GraphicsPanelType
GraphicsPanelTableCellRenderer
GUIFileDAO
GuiUtilities
Header
Header.DatabaseType
HeadlessFileDAO
Helium
HelpDialog
HelpWindow
Histidine
HistogramUtils
Hydrogen
HyperScore
Identification
IdentificationAlgorithmParameter
IdentificationDB
IdentificationMatch
IdentificationMatch.MatchType
IdentificationMethod
IdentificationParameters
IdentificationParametersCLI
IdentificationParametersCLIParams
IdentificationParametersEditionDialog
IdentificationParametersFactory
IdentificationParametersInputBean
IdentificationParametersMarshaller
IdentificationParametersNameDialog
IdentificationParametersOverviewDialog
IdentificationParametersSelectionDialog
IdentificationParametersSelectionDialog.StartupMode
IdfileReader
IdfileReaderFactory
IdMatchValidationPreferences
ImageType
ImmoniumIon
ImmoniumIonAnnotator
ImportSequencesFromDnaDialog
ImportSequencesFromFilesDialog
ImportSequencesFromUniprotDialog
Insertion
InstanceVariables
Instrument
IntensityHistogram
IntensityRankScore
InterfaceAdapter
Iodine
Ion
Ion.IonType
IonFactory
IonFeature
IonFeature.Property
IonLabelColorTableModel
IonMatch
IonMatch.MzErrorType
IonMatchKeysCache
Isoleucine
IsotopeDistributionGui
IsotopicDistribution
IsotopicDistributionPanel
IsotopicDistributionSpectrum
IsotopicElement
IteratorFactory
J
JarFileFilter
JavaHomeDialog
JavaHomeOrMemoryDialogParent
JavaMemoryDialog
JavaSettingsDialog
JExceptionDialog
JFrameForBytes
JLabelAndComponentPanel
JOptionEditorPane
JpegFileFilter
JsonMarshaller
JTableForDB
KeyUtils
KMeansClustering
KMeansClusteringSettings
LastSelectedFolder
Leucine
LinearRegression
ListChooser
Lithium
Logger
Lysine
MapMutex
MarshallableParameter
MarshallableParameter.Type
MascotEnzymeReader
MassCalc
MassCalcServlet
MassErrorBubblePlot
MassErrorPlot
MassGap
MatchesImportFiltersDialog
MatrixContent
MavenJarFile
MDScore
MedianRegression
MemoryConsumptionStatus
MetaDataXMLParser
Methionine
MetricsPrefix
MgfFileFilter
MgfFileIterator
MgfIndex
MgfReader
MirroredSpectraTestDialog
ModelOrganism
Modification
ModificationFactory
ModificationFeature
ModificationFeature.Property
ModificationImplementation
ModificationMatch
ModificationProfile
ModificationsCLI
ModificationsCLIInputBean
ModificationsCLIParams
ModificationsDialog
ModificationTemplate
MolecularElement
MolecularFormula
Monitorable
MonitorableFileInputStream
MonitorableInputStream
MonitorDimension
MS1Spectrum
Ms2Exporter
Ms2FileFilter
Ms2Identification
MS2MzFidelityScore
Ms2pipFeature
MsAmandaIdfileReader
MsAmandaParameters
MsAmandaSettingsDialog
MsConvertParameters
MsConvertParametersDialog
MsExperiment
MsFormat
MsgfParameters
MsgfSettingsDialog
MSnSpectrum
MspReader
MultipleAAPropertyFeature
Mutation
MutationFactory
MutationMatrix
MyriMatchParameters
MyriMatchSettingsDialog
MzDataFileFilter
MzIdentMLIdfileReader
MzIdentMLIdfileReader.RawValueConversionType
MzIdentMLIdfileSearchParametersConverter
MzIdentMLVersion
MzMlFileFilter
MzXmlFileFilter
NeutralLoss
NeutralLossCombination
NeutralLossesMap
Nitrogen
Node
NoDigestionCombinationIterator
NoDigestionIterator
NonSymmetricalNormalDistribution
NormalDistribution
NormalizationFactors
NormalKernelDensityEstimator
NotesDialog
NotificationDialog
NotificationDialogParent
NovorIdfileReader
NovorParameters
NovorSettingsDialog
NucleotideSequence
NucleotideSequenceImpl
ObjectsCache
ObjectsDB
OldProcessingPreferencesDialog
OmssaParameters
OmssaSettingsDialog
OmxFileFilter
OnyaseIdfileReader
OperatingSystemEnum
OutFileFilter
Oxygen
PathKey
PathSettingsDialog
Patient
PatientInformation
PdbBlock
PdbParameter
PdfFileFilter
Peak
PeffFileFilter
PepnovoAssumptionDetails
PepNovoIdfileReader
PepnovoParameters
PepNovoSettingsDialog
Peptide
PeptideAminoAcidFeature
PeptideAssumption
PeptideAssumptionFilter
PeptideDraft
PeptideFeature
PeptideFeature.Property
PeptideFragmentationModel
PeptideFragmentIon
PeptideMapper
PeptideMapperType
PeptideMapping
PeptideMatch
PeptideMatchesIterator
PeptideProteinMapping
PeptideShakerSetupDialog
PeptideSpectrumAnnotator
PeptideVariantsPreferences
PeptideVariantsSettingsDialog
PeptideWithPosition
PepXmlFileFilter
PepxmlIdfileReader
Persistable
PersistableCode
Phenylalanine
PhosphoRS
Phosphorus
PickUp
PklFile
PklFileFilter
PklSpoFileFilter
PkxFileFilter
PngFileFilter
PNovoIdfileReader
PNovoParameters
PNovoSettingsDialog
Precursor
PrecursorAccuracy
PrecursorAnnotator
PrecursorIon
PrecursorMap
PrideFilter
PrideFilterType
PrideMarshaller
PrideObject
PrideObjectsFactory
PrideQuery
PrideWebService
PrideXmlValidator
PrivacySettingsDialog
ProbabilityFilter
ProcessingPreferences
ProcessingPreferences.ProcessingType
ProcessingPreferencesDialog
ProgressDialog
ProgressDialogX
Proline
PropertiesManager
Protein
Protein
ProteinInferencePreferences
ProteinInferenceSettingsDialog
ProteinIteratorUtils
ProteinMatch
ProteinMatchesIterator
ProteinSequencePane
ProteinSequencesManager
ProteinSequencesManagerGUI
ProteinSequencesPreferencesDialog
ProteinTree
ProteinTreeComponentsFactory
ProteomicAnalysis
ProteoWizardFilter
ProteoWizardSetupDialog
Protocol
ProtXmlFileFilter
PsmIterator
PsmScore
PsmScoresEstimator
PsmScoringPreferences
PsmScoringSettingsDialog
PSProcessingPreferences
PTM
PtmChooser
PtmDialog
PTMFactory
PTMFactoryMarshaller
PTMLocalizationParametersDialog
PtmScore
PTMScoringPreferences
PtmSettings
PtmSiteMapping
PtmtableContent
PtmToPrideMap
PushBackStringReader
Pyrrolysine
Quantification
Quantification.QuantificationMethod
QueryType
Rank
Reagent
Reference
ReferenceArea
ReferenceGroup
RegExEnzyme
RegressionStatistics
RelatedIon
ReportEditor
ReporterIon
ReporterIonAnnotator
ReporterIonQuantification
ReporterMethod
ReporterMethodFactory
ReporterSetupDialog
RescalingEvent
Retrievable
RetrievableCode
ROC
Sample
Sample
SampleAnalysisSet
SampleSelection
SearchGuiOutputOption
SearchGuiSetupDialog
SearchParameters
SearchParameters.MassAccuracyType
SearchSettingsDialog
Selenium
Selenocysteine
SelfUpdatingTableModel
Sequence
SequenceContentType
SequenceDbDetailsDialog
SequenceFactory
SequenceFragmentationPanel
SequenceInputType
SequenceIterator
SequenceMatchingPreferences
SequenceMatchingPreferences.MatchingType
SequenceMatchingSettingsDialog
SequenceModificationPanel
SequenceSegment
SequestFragmentationModel
SequestParamsFileFilter
SerializationUtils
Serine
ShotgunProtocol
SimpleLinearRegression
SimpleNoiseDistribution
SimplePeptideAnnotator
SimplePeptideAnnotator.IonSeries
SimpleXmlWriter
SingleAAPropertyFeature
SnrScore
Sodium
SpeciesDialog
SpeciesFactory
SpecificAnnotationSettings
SpecificSingleEnzymeCombinationIterator
SpecificSingleEnzymeIterator
Spectrum
SpectrumAnnotation
SpectrumAnnotator
SpectrumAnnotator.TiesResolution
SpectrumCounting
SpectrumCounting.SpectrumCountingMethod
SpectrumFactory
SpectrumFile
SpectrumIdentificationAssumption
SpectrumIndex
SpectrumMatch
SpectrumPanel
SpectrumPanelListener
SplashScreen
StandardMasses
StandardUnit
StartBrowser
StartEndPosition
StreamGobbler
StringListChooser
Substitution
Sulfur
SvgFileFilter
Swap
SwingUtils
SwingWorker
TableMap
TableMouseWheelListener
TableProperties
TableScrollBarListener
TableSorter
TableValueWrapper
Tag
TagAssumption
TagComponent
TagFactory
TagFragmentIon
TagMatcher
TagSpectrumAnnotator
TarUtils
TaxonomyTreeDialog
TaxonomyTreePanel
TempFilesManager
TestCaseLM
TextWriter
Threonine
TideIdfileReader
TideParameters
TideSettingsDialog
TiffFileFilter
TimestampRenderer
ToolFactory
ToolTipComboBoxRenderer
Translate
Tryptophan
Tyrosine
UniformFragmentation
UniProtQuery
UniprotTaxonomy
UniprotTaxonomyProvider
UnitOfMeasurement
UnknownElementMassException
UnspecificCombinationIterator
UnspecificIterator
Updateable
UpdateableCode
UrParameter
Util
UtilitiesDemo
UtilitiesGUIDefaults
UtilitiesPathPreferences
UtilitiesPathPreferences.UtilitiesPathKey
UtilitiesUserPreferences
ValidationQCPreferences
ValidationQCPreferencesDialog
ValidationQCPreferencesDialogParent
ValidationSettingsDialog
Valine
Variant
VariantMatch
VennDiagram
VennDiagramDialog
VennDiagramLegendLocationDialog
VennDiagramPanel
VennDiagramPanel.VennDiagramType
VisibleTableColumnsDialog
VisibleTableColumnsDialogParent
WaitingActionListener
WaitingDialog
WaitingDialogExceptionHandler
WaitingHandler
WaitingHandlerCLIImpl
WaitingHandlerDummy
WaveletTree
WebDAO
WorkbookStyle
X
XmlFileFilter
XMLValidationErrorHandler
XtandemParameters
XTandemSettingsDialog
XYPlotFiltersDialog
XYPlottingDialog
XYPlottingDialog.PlottingDialogPlotType
XYZDataPoint
Z
ZipUtils